[gmx-users] gromacs 2018 compilation problem with stdlib

Mark Abraham mark.j.abraham at gmail.com
Mon Jul 16 10:09:57 CEST 2018


On Sat, Jul 14, 2018 at 4:58 AM Manoel Barrionuevo <manoelvfb at gmail.com>

> Hi all,
> I'm trying to compile gromacs 2018.2 and I would like to use intel
> compilers along with nvidia gpu graphic (GTX 1060) card in a desktop
> computer with a intel i5 quad-core cpu (the only purpose of it is for
> learning), in order to do so I was first following the suggested
> procedures at the INSTALL file distributed along with gromacs, and got
> the command bellow:
> cmake ../ -DGMX_FFT_LIBRARY="mkl" -DMKL_LIBRARIES="-Wl,--start-group
> /opt/intel17/mkl/lib/intel64/libmkl_intel_ilp64.a
> /opt/intel17/mkl/lib/intel64/libmkl_gnu_thread.a
> /opt/intel17/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp
> -lpthread -lm -ldl" -DMKL_INCLUDE_DIR="/opt/intel17/mkl/include"
> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/"
> -std=c++11"

You're doing a few things that make your life hard (or are brittle) and
some that make things slow. Source the appropriate script for the intel
compiler that you want, and then leave MKL details up to it. Choosing -O2
for optimization overrides the defaults for no good reason. Thus

source /path/to/compiler/bin/compilervars.sh intel64
cmake ../ -DGMX_FFT_LIBRARY="mkl" -DGMX_GPU=on

It worths to say that the OS under current operation is Lubuntu (16.04)
> and it has both gcc-5.4.1 and g++-5.4.1. Everything goes smoothly
> without problems, however I noticed a std failure after issuing the
> "make" command, it says:
> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(250):
> error: namespace "std" has no member "_Exit"
>        std:: _Exit(returnValue);
>              ^
> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(251):
> warning #1628: function declared with "noreturn" does retu
> rn
>    }
>    ^
> The same problem can be seen if I start from a very simple "cmake ../"
> and "make". What am I doing wrong? Is there some environment preparation
> step to be done prior to everything else, and what should it be?

On Linux, Intel compilers rely on having and finding a suitable gcc for the
standard library, so I can only presume something is messed up there. For
example, gcc was installed or updated after icc. Try the advice at


> I must say that I'm not an expert on compiling things up and I got
> stuck. Could someone help me out? It would be of great help to know some
> tips from you guys.
> Thank you all.
> Kind regards,
> --
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